Entering edit mode
9.2 years ago
nikhilvgbt
•
0
Hi,
I am trying to run cuffmerge but I am getting the following error. Could you please tell me the what the problem is and how can I solve this error?
This is the command I used for cuffmerge:
cuffmerge -g hg19.gtf -s hg19.fa -p 8 assemblies.txt
and main error is:
[Mon Jan 26 22:40:49 2015] Beginning transcriptome assembly merge
-------------------------------------------
[Mon Jan 26 22:40:49 2015] Preparing output location ./merged_asm/
[Mon Jan 26 22:40:55 2015] Converting GTF files to SAM
[22:40:55] Loading reference annotation.
[22:40:56] Loading reference annotation.
[Mon Jan 26 22:40:58 2015] Quantitating transcripts
Warning: Your version of Cufflinks is not up-to-date. It is recommended that you upgrade to Cufflinks v2.2.1 to benefit from the most recent features and bug fixes (http://cufflinks.cbcb.umd.edu).
Command line:
cufflinks -o ./merged_asm/ -F 0.05 -g hg19.gtf -q --overhang-tolerance 200 --library-type=transfrags -A 0.0 --min-frags-per-transfrag 0 --no-5-extend -p 8 ./merged_asm/tmp/mergeSam_fileMgq1Io
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
File ./merged_asm/tmp/mergeSam_fileMgq1Io doesn't appear to be a valid BAM file, trying SAM...
[22:40:59] Loading reference annotation.
[FAILED]
Error: could not execute cufflinks
Do you have the hg19.gtf file in the folder you're running cufflinks in?
@RamRS
I have both the files .gtf and .fa files in working directory, but when I run the command the error is shown.
Did you check the link from my other comment?
Also, take a look at this: http://seqanswers.com/forums/showthread.php?t=11694
Hi RamRS:
I checked that in forum and I tried accordingly but still same error. As far as I understood there is problem in the output of tophat which is .bam file or else output of the Cufflinks ...
Could you also give us the exact command you used?
Are you using .gtf and .fa from same source?
Ah yeah the old problem.